yidingfang / qp-shotgun

Shotgun Qiita Plugin

Qiita (canonically pronounced cheetah) is an analysis environment for microbiome (and other "comparative -omics") datasets.

This package includes the Shotgun functionality for Qiita. Currently, we have:

• HUMAnN2

Note that is suggested that you download the full databases once this package is installed by:

$ humann2_databases --download chocophlan full $DIR
$ humann2_databases --download uniref diamond $DIR

The default pipeline is:

1. Run HUMAnN2 on per sample FASTQ
2. Collate individual results into single OTU tables: gene families, path coverage and path abundance.
3. Renormalize the tables: gene families - CPM, path coverage - relative abundance, path abundance - relative abundance.
4. Stratify the renormalized tables.

• `KneadData <https://bitbucket.org/biobakery/kneaddata/wiki/Home`_

Note that: - HUMAnN2 depends on metaphlan2 but neither the HUMAnN2 or this plugin automatically install that dependency. Remember that you need to put the db_v20 folder in the path that the metaphlan2.py executable. - KneadData depends on fastqc and trimmomatic but neither the KneadData or this plugin automatically install that dependency.